[ARVADOS] updated: 2509f755a36b2fc944689d5a1ea62729d4d6c3a5
git at public.curoverse.com
git at public.curoverse.com
Mon Aug 18 18:59:36 EDT 2014
Summary of changes:
.gitignore | 4 +-
.../app/assets/javascripts/infinite_scroll.js | 3 +-
.../app/assets/javascripts/user_agreements.js | 9 +
.../app/controllers/application_controller.rb | 137 ++++++---
.../app/controllers/collections_controller.rb | 3 +-
.../app/controllers/projects_controller.rb | 82 ++++--
.../app/controllers/user_agreements_controller.rb | 1 +
apps/workbench/app/controllers/users_controller.rb | 24 +-
apps/workbench/app/helpers/application_helper.rb | 2 +-
apps/workbench/app/models/user.rb | 6 +
.../app/views/application/_choose.html.erb | 13 +-
.../app/views/application/_content.html.erb | 3 +-
.../app/views/application/_content_layout.html.erb | 15 +-
.../views/application/_tab_line_buttons.html.erb | 0
apps/workbench/app/views/application/show.html.erb | 1 -
.../app/views/collections/_show_files.html.erb | 5 -
.../app/views/collections/_show_recent.html.erb | 13 -
.../workbench/app/views/collections/index.html.erb | 14 +
apps/workbench/app/views/collections/show.html.erb | 7 +-
.../app/views/keep_disks/_content_layout.html.erb | 4 +-
apps/workbench/app/views/layouts/body.html.erb | 6 +
.../views/pipeline_instances/_show_recent.html.erb | 7 -
.../app/views/pipeline_instances/index.html.erb | 8 +
.../pipeline_templates/_show_components.html.erb | 17 --
.../{_show_components.html.erb => show.html.erb} | 2 +-
.../views/projects/_show_contents_rows.html.erb | 18 +-
.../views/projects/_show_data_collections.html.erb | 72 +----
.../projects/_show_jobs_and_pipelines.html.erb | 11 +-
.../views/projects/_show_other_objects.html.erb | 11 +-
.../projects/_show_pipeline_templates.html.erb | 11 +-
.../app/views/projects/_show_sharing.html.erb | 10 +-
.../app/views/projects/_show_subprojects.html.erb | 11 +-
.../app/views/projects/_show_tab_contents.html.erb | 27 +-
...how_data_collections.html.erb => show.html.erb} | 9 +-
.../app/views/user_agreements/index.html.erb | 22 +-
apps/workbench/app/views/users/inactive.html.erb | 4 +
apps/workbench/app/views/users/profile.html.erb | 95 ++++++
apps/workbench/config/application.default.yml | 57 ++++
apps/workbench/config/routes.rb | 2 +
.../test/functional/application_controller_test.rb | 18 ++
.../test/functional/collections_controller_test.rb | 2 +-
.../test/functional/projects_controller_test.rb | 91 +++++-
.../test/functional/users_controller_test.rb | 6 +
.../test/integration/application_layout_test.rb | 317 +++++++++++++++++++++
.../workbench/test/integration/collections_test.rb | 24 +-
.../test/integration/pipeline_instances_test.rb | 5 +-
apps/workbench/test/integration/projects_test.rb | 12 +-
apps/workbench/test/test_helper.rb | 3 +
crunch_scripts/arvados-bcbio-nextgen.py | 2 +-
crunch_scripts/collection-merge | 41 +--
.../crunchutil}/__init__.py | 0
crunch_scripts/crunchutil/robust_put.py | 48 ++++
crunch_scripts/{ => crunchutil}/subst.py | 8 +-
crunch_scripts/crunchutil/vwd.py | 54 ++++
crunch_scripts/decompress-all.py | 61 ++++
crunch_scripts/run-command | 216 ++++++++++----
crunch_scripts/split-fastq.py | 128 +++++++++
doc/_config.yml | 4 +-
...py.liquid => _concurrent_hash_script_py.liquid} | 0
doc/api/methods/collections.html.textile.liquid | 3 +
doc/sdk/go/index.html.textile.liquid | 65 +++++
doc/sdk/index.html.textile.liquid | 1 +
.../topics/tutorial-job-debug.html.textile.liquid | 163 -----------
.../topics/tutorial-parallel.html.textile.liquid | 22 +-
.../tutorial-trait-search.html.textile.liquid | 44 +--
.../tutorial-firstscript.html.textile.liquid | 165 ++++-------
.../tutorials/tutorial-keep.html.textile.liquid | 4 +-
...uid => tutorial-submit-job.html.textile.liquid} | 11 +-
docker/build_tools/Makefile | 16 +-
docker/build_tools/config.rb | 7 +-
docker/jobs/Dockerfile | 4 +-
docker/keep/Dockerfile | 13 +-
docker/keep/run-keep.in | 2 +-
sdk/cli/bin/arv | 8 +-
sdk/cli/bin/arv-run-pipeline-instance | 69 +++--
sdk/cli/bin/crunch-job | 27 +-
.../sdk/sdk.go => arvadosclient/arvadosclient.go} | 2 +-
.../arvadosclient_test.go} | 7 +-
sdk/go/go.sh | 17 --
.../{src/arvados.org => }/keepclient/hashcheck.go | 5 +-
.../arvados.org => }/keepclient/hashcheck_test.go | 0
.../{src/arvados.org => }/keepclient/keepclient.go | 8 +-
.../arvados.org => }/keepclient/keepclient_test.go | 63 ++--
sdk/go/{src/arvados.org => }/keepclient/support.go | 2 +-
sdk/go/{src/arvados.org => }/streamer/streamer.go | 0
.../arvados.org => }/streamer/streamer_test.go | 0
sdk/go/{src/arvados.org => }/streamer/transfer.go | 0
sdk/python/.gitignore | 2 +-
sdk/python/arvados/__init__.py | 11 +
sdk/python/arvados/api.py | 136 +++++----
sdk/python/arvados/collection.py | 23 +-
sdk/python/arvados/commands/put.py | 1 -
sdk/python/arvados/events.py | 8 +-
sdk/python/arvados/keep.py | 54 ++--
sdk/python/arvados/stream.py | 1 -
sdk/python/bin/arv-get | 58 ++--
sdk/python/bin/arv-ls | 3 -
sdk/python/bin/arv-normalize | 3 -
sdk/python/bin/arv-ws | 8 +-
sdk/python/tests/run_test_server.py | 48 +---
sdk/python/tests/test_api.py | 21 +-
sdk/python/tests/test_arv_put.py | 6 +-
sdk/ruby/lib/arvados.rb | 20 +-
services/api/Gemfile.lock | 14 +-
.../api/app/controllers/application_controller.rb | 12 +-
.../arvados/v1/collections_controller.rb | 85 +++---
.../app/controllers/arvados/v1/jobs_controller.rb | 18 ++
.../arvados/v1/repositories_controller.rb | 10 +-
.../controllers/arvados/v1/schema_controller.rb | 57 ++--
.../app/controllers/arvados/v1/users_controller.rb | 16 +-
services/api/app/mailers/profile_notifier.rb | 8 +
services/api/app/models/arvados_model.rb | 22 ++
services/api/app/models/collection.rb | 7 +-
services/api/app/models/job.rb | 2 +-
services/api/app/models/user.rb | 63 ++--
.../profile_notifier/profile_created.text.erb | 2 +
services/api/config/application.default.yml | 6 +
services/api/script/crunch-dispatch.rb | 42 ++-
.../test/fixtures/api_client_authorizations.yml | 12 +
services/api/test/fixtures/jobs.yml | 11 +
services/api/test/fixtures/pipeline_instances.yml | 5 +
services/api/test/fixtures/users.yml | 61 +++-
.../arvados/v1/collections_controller_test.rb | 47 ++-
.../functional/arvados/v1/users_controller_test.rb | 73 +++++
services/crunch/crunchstat/go.sh | 15 -
.../src/arvados.org => }/crunchstat/crunchstat.go | 0
services/fuse/arvados_fuse/__init__.py | 20 +-
services/fuse/bin/arv-mount | 50 ++--
services/keep/go.sh | 17 --
.../src/arvados.org => }/keepproxy/keepproxy.go | 6 +-
.../arvados.org => }/keepproxy/keepproxy_test.go | 42 ++-
.../{keep/src/keep => keepstore}/handler_test.go | 0
services/{keep/src/keep => keepstore}/handlers.go | 0
.../src/keep/keep.go => keepstore/keepstore.go} | 0
.../keep_test.go => keepstore/keepstore_test.go} | 11 +-
services/{keep/src/keep => keepstore}/perms.go | 0
.../{keep/src/keep => keepstore}/perms_test.go | 0
services/{keep/src/keep => keepstore}/volume.go | 0
.../{keep/src/keep => keepstore}/volume_unix.go | 0
.../src/keep => keepstore}/volume_unix_test.go | 0
140 files changed, 2440 insertions(+), 1211 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/user_agreements.js
copy services/fuse/tests/__init__.py => apps/workbench/app/views/application/_tab_line_buttons.html.erb (100%)
create mode 100644 apps/workbench/app/views/collections/index.html.erb
create mode 100644 apps/workbench/app/views/pipeline_instances/index.html.erb
copy apps/workbench/app/views/pipeline_templates/{_show_components.html.erb => show.html.erb} (93%)
copy apps/workbench/app/views/projects/{_show_data_collections.html.erb => show.html.erb} (86%)
create mode 100644 apps/workbench/app/views/users/profile.html.erb
create mode 100644 apps/workbench/test/integration/application_layout_test.rb
copy {services/fuse/tests => crunch_scripts/crunchutil}/__init__.py (100%)
create mode 100644 crunch_scripts/crunchutil/robust_put.py
rename crunch_scripts/{ => crunchutil}/subst.py (91%)
create mode 100644 crunch_scripts/crunchutil/vwd.py
create mode 100755 crunch_scripts/decompress-all.py
create mode 100755 crunch_scripts/split-fastq.py
rename doc/_includes/{_parallel_hash_script_py.liquid => _concurrent_hash_script_py.liquid} (100%)
create mode 100644 doc/sdk/go/index.html.textile.liquid
delete mode 100644 doc/user/topics/tutorial-job-debug.html.textile.liquid
copy doc/user/tutorials/{tutorial-firstscript.html.textile.liquid => tutorial-submit-job.html.textile.liquid} (90%)
rename sdk/go/{src/arvados.org/sdk/sdk.go => arvadosclient/arvadosclient.go} (99%)
rename sdk/go/{src/arvados.org/sdk/sdk_test.go => arvadosclient/arvadosclient_test.go} (95%)
delete mode 100755 sdk/go/go.sh
rename sdk/go/{src/arvados.org => }/keepclient/hashcheck.go (98%)
rename sdk/go/{src/arvados.org => }/keepclient/hashcheck_test.go (100%)
rename sdk/go/{src/arvados.org => }/keepclient/keepclient.go (97%)
rename sdk/go/{src/arvados.org => }/keepclient/keepclient_test.go (92%)
rename sdk/go/{src/arvados.org => }/keepclient/support.go (99%)
rename sdk/go/{src/arvados.org => }/streamer/streamer.go (100%)
rename sdk/go/{src/arvados.org => }/streamer/streamer_test.go (100%)
rename sdk/go/{src/arvados.org => }/streamer/transfer.go (100%)
create mode 100644 services/api/app/mailers/profile_notifier.rb
create mode 100644 services/api/app/views/profile_notifier/profile_created.text.erb
delete mode 100755 services/crunch/crunchstat/go.sh
rename services/{crunch/crunchstat/src/arvados.org => }/crunchstat/crunchstat.go (100%)
delete mode 100755 services/keep/go.sh
rename services/{keep/src/arvados.org => }/keepproxy/keepproxy.go (98%)
rename services/{keep/src/arvados.org => }/keepproxy/keepproxy_test.go (85%)
rename services/{keep/src/keep => keepstore}/handler_test.go (100%)
rename services/{keep/src/keep => keepstore}/handlers.go (100%)
rename services/{keep/src/keep/keep.go => keepstore/keepstore.go} (100%)
rename services/{keep/src/keep/keep_test.go => keepstore/keepstore_test.go} (97%)
rename services/{keep/src/keep => keepstore}/perms.go (100%)
rename services/{keep/src/keep => keepstore}/perms_test.go (100%)
rename services/{keep/src/keep => keepstore}/volume.go (100%)
rename services/{keep/src/keep => keepstore}/volume_unix.go (100%)
rename services/{keep/src/keep => keepstore}/volume_unix_test.go (100%)
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commit 2509f755a36b2fc944689d5a1ea62729d4d6c3a5
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Aug 18 18:19:29 2014 -0400
3114: Follow return_to param, if given, when redirecting users#show to projects#show.
Don't redirect non-html requests.
diff --git a/apps/workbench/app/controllers/users_controller.rb b/apps/workbench/app/controllers/users_controller.rb
index 189f295..27f13b7 100644
--- a/apps/workbench/app/controllers/users_controller.rb
+++ b/apps/workbench/app/controllers/users_controller.rb
@@ -7,7 +7,11 @@ class UsersController < ApplicationController
def show
if params[:uuid] == current_user.uuid
- redirect_to project_path(params[:uuid])
+ respond_to do |f|
+ f.html do
+ redirect_to(params[:return_to] || project_path(params[:uuid]))
+ end
+ end
else
super
end
commit 903e49f38401ed6113f4e0ec159db8750d4db2ba
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Aug 18 18:18:55 2014 -0400
3114: Update test case: searching for own uuid now shows home project.
diff --git a/apps/workbench/test/integration/application_layout_test.rb b/apps/workbench/test/integration/application_layout_test.rb
index 78842a4..19bb4c1 100644
--- a/apps/workbench/test/integration/application_layout_test.rb
+++ b/apps/workbench/test/integration/application_layout_test.rb
@@ -213,8 +213,8 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
page.find('.glyphicon-search').click
end
- # we should now be in the user's page as a result of search
- assert page.has_text? user['first_name']
+ # we should now be in the user's home project as a result of search
+ assert_selector "#Data_collections[data-object-uuid='#{user['uuid']}']"
# let's search again for an invalid valid uuid
within('.navbar-fixed-top') do
commit d81ea65da05119d5c6480d373b5d42bbee8ae1ad
Merge: f7768d3 8917fa8
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Aug 18 18:02:47 2014 -0400
3114: Merge branch 'master' into 3114-copy-to-project
diff --cc apps/workbench/app/controllers/application_controller.rb
index 1607303,b626361..98bc53a
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@@ -174,12 -202,10 +202,10 @@@ class ApplicationController < ActionCon
return render_not_found("object not found")
end
respond_to do |f|
- f.json { render json: @object.attributes.merge(href: url_for(@object)) }
+ f.json { render json: @object.attributes.merge(href: url_for(action: :show, id: @object)) }
f.html {
if params['tab_pane']
- comparable = self.respond_to? :compare
- render(partial: 'show_' + params['tab_pane'].downcase,
- locals: { comparable: comparable, objects: @objects })
+ render_pane params['tab_pane']
elsif request.method.in? ['GET', 'HEAD']
render
else
diff --cc apps/workbench/app/controllers/users_controller.rb
index d817b32,eb07fc3..189f295
--- a/apps/workbench/app/controllers/users_controller.rb
+++ b/apps/workbench/app/controllers/users_controller.rb
@@@ -1,19 -1,13 +1,21 @@@
class UsersController < ApplicationController
- skip_before_filter :find_object_by_uuid, :only => [:welcome, :activity, :storage]
+ skip_around_filter :require_thread_api_token, only: :welcome
+ skip_before_filter :check_user_agreements, only: [:welcome, :inactive]
+ skip_before_filter :check_user_profile, only: [:welcome, :inactive, :profile]
+ skip_before_filter :find_object_by_uuid, only: [:welcome, :activity, :storage]
before_filter :ensure_current_user_is_admin, only: [:sudo, :unsetup, :setup]
+ def show
+ if params[:uuid] == current_user.uuid
+ redirect_to project_path(params[:uuid])
+ else
+ super
+ end
+ end
+
def welcome
if current_user
- params[:action] = 'home'
- home
+ redirect_to (params[:return_to] || '/')
end
end
commit f7768d3dbc6e4c4fa56cbe4906d6682120b8daa3
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Aug 18 16:51:13 2014 -0400
3114: Fix href in json response for generic #create action too. See 7485476.
diff --git a/apps/workbench/app/controllers/application_controller.rb b/apps/workbench/app/controllers/application_controller.rb
index e38a32d..1607303 100644
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@ -248,7 +248,7 @@ class ApplicationController < ActionController::Base
@object ||= model_class.new @new_resource_attrs, params["options"]
if @object.save
respond_to do |f|
- f.json { render json: @object.attributes.merge(href: url_for(@object)) }
+ f.json { render json: @object.attributes.merge(href: url_for(action: :show, id: @object)) }
f.html {
redirect_to @object
}
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